assessPool analysis

Coverage cutoff: ≥10

Abstract

This report summarizes the output of population genetic analyses of a pool-seq RAD library.

Filtering

Stepwise filtering reuslts

SNPs remaining after each filtering step.

Note: filtering results displayed are independent, not cumulative.

Filter options with no effect: max_missing, min_mean_depth, min_pools.

Cumulative filtering results

SNPs remaining after each filtering step.

Cumulative filter results
(Note: filtered SNP count may differ from SNP counts associated with F_st calculations).

High-level summaries

grenedalf

All SNPs

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

SNPs shared by all pools

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

poolfstat

All SNPs

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

SNPs shared by all pools

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

popoolation

All SNPs

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

SNPs shared by all pools

Plot

Global summary statistics by coverage cutoff

Table

Global summary statistics by coverage cutoff

Pairwise F_st by minimum coverage

grenedalf

All SNPs

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

SNPs shared by all pools

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

poolfstat

All SNPs

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

SNPs shared by all pools

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

popoolation

All SNPs

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

SNPs shared by all pools

Scatter plot (means)

Box plot (distributions)

Note: subsampled to 30 outliers per pair.

Summary statistic heatmaps

grenedalf

All SNPs

F_st (±SD)

Lower triangle: mean pairwise F_st
Upper triangle: standard deviation of F_st

Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to F_st calculation
Upper triangle: average shared SNPs per contig

Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation

Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs

Note: Grey cells indicate missing data.

SNPs shared by all pools

F_st (±SD)

Lower triangle: mean pairwise F_st
Upper triangle: standard deviation of F_st

Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to F_st calculation
Upper triangle: average shared SNPs per contig

Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation

Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs

Note: Grey cells indicate missing data.

poolfstat

All SNPs

F_st (±SD)

Lower triangle: mean pairwise F_st
Upper triangle: standard deviation of F_st

Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to F_st calculation
Upper triangle: average shared SNPs per contig

Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation

Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs

Note: Grey cells indicate missing data.

SNPs shared by all pools

F_st (±SD)

Lower triangle: mean pairwise F_st
Upper triangle: standard deviation of F_st

Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to F_st calculation
Upper triangle: average shared SNPs per contig

Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation

Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs

Note: Grey cells indicate missing data.

popoolation

All SNPs

F_st (±SD)

Lower triangle: mean pairwise F_st
Upper triangle: standard deviation of F_st

Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to F_st calculation
Upper triangle: average shared SNPs per contig

Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation

Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs

Note: Grey cells indicate missing data.

SNPs shared by all pools

F_st (±SD)

Lower triangle: mean pairwise F_st
Upper triangle: standard deviation of F_st

Note: Grey cells indicate missing data.

SNPs / SNPs per contig

Lower triangle: pairwise shared SNPs contributing to F_st calculation
Upper triangle: average shared SNPs per contig

Note: Grey cells indicate missing data.

Mean coverage (±SD)

Lower triangle: mean pairwise coverage
Upper triangle: pairwise coverage standard deviation

Note: Grey cells indicate missing data.

Contigs

Pairwise shared contigs

Note: Grey cells indicate missing data.

F_st method correlations

grenedalf vs poolfstat

Note: Due to potentially large datasets, only a subsample of 1,000 F_st values is shown here.

grenedalf vs popoolation

Note: Due to potentially large datasets, only a subsample of 1,000 F_st values is shown here.

poolfstat vs popoolation

Note: Due to potentially large datasets, only a subsample of 1,000 F_st values is shown here.

Fisher’s test plots

Fisher test results are presented as static plots since these datasets can get huge, making plotly go slow or crash.

assesspool

Points above red line indicate p < 0.05.

popoolation

Points above red line indicate p < 0.05.